"""
velvet datatypes
James E Johnson - University of Minnesota
for velvet assembler tool in galaxy
"""

import logging
import os
import re
import sys

from galaxy.datatypes import data
from galaxy.datatypes import sequence
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.sniff import build_sniff_from_prefix
from galaxy.datatypes.text import Html

log = logging.getLogger(__name__)


@build_sniff_from_prefix
class Amos(data.Text):
    """Class describing the AMOS assembly file """
    edam_data = "data_0925"
    edam_format = "format_3582"
    file_ext = 'afg'

    def sniff_prefix(self, file_prefix):
        """
        Determines whether the file is an amos assembly file format
        Example::

          {CTG
          iid:1
          eid:1
          seq:
          CCTCTCCTGTAGAGTTCAACCGA-GCCGGTAGAGTTTTATCA
          .
          qlt:
          DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD
          .
          {TLE
          src:1027
          off:0
          clr:618,0
          gap:
          250 612
          .
          }
          }
        """
        for line in file_prefix.line_iterator():
            if not line:
                break  # EOF
            line = line.strip()
            if line:  # first non-empty line
                if line.startswith('{'):
                    if re.match(r'{(RED|CTG|TLE)$', line):
                        return True
        return False


@build_sniff_from_prefix
class Sequences(sequence.Fasta):
    """Class describing the Sequences file generated by velveth """
    edam_data = "data_0925"
    file_ext = 'sequences'

    def sniff_prefix(self, file_prefix):
        """
        Determines whether the file is a velveth produced  fasta format
        The id line has 3 fields separated by tabs: sequence_name  sequence_index category::

          >SEQUENCE_0_length_35   1       1
          GGATATAGGGCCAACCCAACTCAACGGCCTGTCTT
          >SEQUENCE_1_length_35   2       1
          CGACGAATGACAGGTCACGAATTTGGCGGGGATTA
        """
        fh = file_prefix.string_io()
        while True:
            line = fh.readline()
            if not line:
                break  # EOF
            line = line.strip()
            if line:  # first non-empty line
                if line.startswith('>'):
                    if not re.match(r'>[^\t]+\t\d+\t\d+$', line):
                        break
                    # The next line.strip() must not be '', nor startwith '>'
                    line = fh.readline().strip()
                    if line == '' or line.startswith('>'):
                        break
                    return True
                else:
                    break  # we found a non-empty line, but it's not a fasta header
        return False


@build_sniff_from_prefix
class Roadmaps(data.Text):
    """Class describing the Sequences file generated by velveth """
    edam_format = "format_2561"
    file_ext = 'roadmaps'

    def sniff_prefix(self, file_prefix):
        """
        Determines whether the file is a velveth produced RoadMap::
          142858  21      1
          ROADMAP 1
          ROADMAP 2
          ...
        """

        fh = file_prefix.string_io()
        while True:
            line = fh.readline()
            if not line:
                break  # EOF
            line = line.strip()
            if line:  # first non-empty line
                if not re.match(r'\d+\t\d+\t\d+$', line):
                    break
                # The next line.strip() should be 'ROADMAP 1'
                line = fh.readline().strip()
                if not re.match(r'ROADMAP \d+$', line):
                    break
                return True
            else:
                break  # we found a non-empty line, but it's not a fasta header
        return False


class Velvet(Html):
    MetadataElement(name="base_name", desc="base name for velveth dataset", default="velvet", readonly=True, set_in_upload=True)
    MetadataElement(name="paired_end_reads", desc="has paired-end reads", default="False", readonly=False, set_in_upload=True)
    MetadataElement(name="long_reads", desc="has long reads", default="False", readonly=False, set_in_upload=True)
    MetadataElement(name="short2_reads", desc="has 2nd short reads", default="False", readonly=False, set_in_upload=True)
    composite_type = 'auto_primary_file'
    file_ext = 'velvet'

    def __init__(self, **kwd):
        super().__init__(**kwd)
        self.add_composite_file('Sequences', mimetype='text/html', description='Sequences', substitute_name_with_metadata=None, is_binary=False)
        self.add_composite_file('Roadmaps', mimetype='text/html', description='Roadmaps', substitute_name_with_metadata=None, is_binary=False)
        self.add_composite_file('Log', mimetype='text/html', description='Log', optional='True', substitute_name_with_metadata=None, is_binary=False)

    def generate_primary_file(self, dataset=None):
        log.debug("Velvet log info  {} {}".format('JJ generate_primary_file', dataset))
        rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
        for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
            fn = composite_name
            log.debug("Velvet log info  {} {} {}".format('JJ generate_primary_file', fn, composite_file))
            opt_text = ''
            if composite_file.optional:
                opt_text = ' (optional)'
            if composite_file.get('description'):
                rval.append('<li><a href="{}" type="text/plain">{} ({})</a>{}</li>'.format(fn, fn, composite_file.get('description'), opt_text))
            else:
                rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
        rval.append('</ul></div></html>')
        return "\n".join(rval)

    def regenerate_primary_file(self, dataset):
        """
        cannot do this until we are setting metadata
        """
        log.debug("Velvet log info  %s" % 'JJ regenerate_primary_file')
        gen_msg = ''
        try:
            efp = dataset.extra_files_path
            log_path = os.path.join(efp, 'Log')
            with open(log_path) as f:
                log_content = f.read(1000)
            log_msg = re.sub(r'/\S*/', '', log_content)
            log.debug("Velveth log info  %s" % log_msg)
            paired_end_reads = re.search(r'-(short|long)Paired', log_msg) is not None
            dataset.metadata.paired_end_reads = paired_end_reads
            long_reads = re.search(r'-long', log_msg) is not None
            dataset.metadata.long_reads = long_reads
            short2_reads = re.search(r'-short(Paired)?2', log_msg) is not None
            dataset.metadata.short2_reads = short2_reads
            dataset.info = re.sub(r'.*velveth \S+', 'hash_length', re.sub(r'\n', ' ', log_msg))
            if paired_end_reads:
                gen_msg = gen_msg + ' Paired-End Reads'
            if long_reads:
                gen_msg = gen_msg + ' Long Reads'
            if len(gen_msg) > 0:
                gen_msg = 'Uses: ' + gen_msg
        except Exception:
            log.debug("Velveth could not read Log file in %s" % efp)
        log.debug("Velveth log info  %s" % gen_msg)
        rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
        # rval.append('<div>Generated:<p/><code> %s </code></div>' %(re.sub('\n','<br>',log_msg)))
        rval.append('<div>Generated:<p/> %s </div>' % (gen_msg))
        rval.append('<div>Velveth dataset:<p/><ul>')
        for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
            fn = composite_name
            log.debug("Velvet log info  {} {} {}".format('JJ regenerate_primary_file', fn, composite_file))
            if re.search('Log', fn) is None:
                opt_text = ''
                if composite_file.optional:
                    opt_text = ' (optional)'
                if composite_file.get('description'):
                    rval.append('<li><a href="{}" type="text/plain">{} ({})</a>{}</li>'.format(fn, fn, composite_file.get('description'), opt_text))
                else:
                    rval.append(f'<li><a href="{fn}" type="text/plain">{fn}</a>{opt_text}</li>')
        rval.append('</ul></div></html>')
        with open(dataset.file_name, 'w') as f:
            f.write("\n".join(rval))
            f.write('\n')

    def set_meta(self, dataset, **kwd):
        Html.set_meta(self, dataset, **kwd)
        self.regenerate_primary_file(dataset)


if __name__ == '__main__':
    import doctest
    doctest.testmod(sys.modules[__name__])
